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Repeatome Analysis of Plasma Circulating DNA in Patients with Cardiovascular Disease: Variation with Cell-Free DNA

Stefania Fumarola1, Monia Cecati2, Francesca Marchegiani3

  • 1Advanced Technology Center for Aging Research, IRCCS INRCA, 60121 Ancona, Italy.

International Journal of Molecular Sciences
|July 29, 2025
PubMed

Insights

Low-pass next-generation sequencing (NGS) reveals repetitive DNA patterns in cell-free DNA (cfDNA). Specific repetitive elements correlate with cardiovascular disease biomarkers and comorbidities, offering new diagnostic potential.

Area of Science:

  • Genomics
  • Molecular Biology
  • Biochemistry

Background:

  • Repetitive DNA constitutes over 50% of the human genome and is found in circulating cell-free DNA (cfDNA).
  • Previous research indicated cfDNA levels and integrity predict survival in elderly cardiovascular disease patients.
  • The characterization of cfDNA repeat content using low-pass next-generation sequencing (NGS) requires further investigation.

Purpose of the Study:

  • To determine if low-pass NGS can characterize the repeat content of cfDNA.
  • To analyze the occurrence of repetitive DNA subfamilies in different cfDNA size fractions.
  • To explore correlations between cfDNA repeat abundance and prognostic biomarkers in cardiovascular disease.

Main Methods:

  • Analysis of cfDNA samples from 24 heart failure patients using low-pass NGS.
  • Separation of cfDNA into dinucleosomal (>250 bp) and mononucleosomal (≤250 bp) fractions.
  • Quantification and comparison of repetitive DNA subfamily abundance in each fraction.

Main Results:

  • Alu repetitive elements were more abundant in the dinucleosomal cfDNA fraction.
  • Alpha satellites were enriched in the mononucleosomal cfDNA fraction.
  • Relative abundance of Alu, ALR, and L1HS DNA in the dinucleosomal fraction correlated with prognostic biomarkers; Alu DNA showed a negative association with chronic kidney disease.

Conclusions:

  • Low-pass NGS is a cost-effective method for analyzing the cfDNA repeat landscape.
  • The composition of plasma cfDNA may be influenced by various mechanisms in different physiological and pathological conditions.
  • Characterizing cfDNA repeat content could identify novel biomarkers for cardiovascular disease.

Keywords:
Alu elementsCKDcardiovascular diseasecfDNAcirculating biomarkerseGFRhearth failurelow-pass NGSrepetitive DNA

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